9P14 | pdb_00009p14

Thaumatin Room-Temperature In-Situ, Grown On-Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.190 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.159 (Depositor), 0.157 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Does crossing the pond affect crystal quality?

Campomizzi, C.S.Snell, M.E.Mikolajek, H.Sandy, J.Sanchez-Weatherby, J.Budziszewski, G.R.Russi, S.Howells Jr., R.Cohen, A.Hough, M.A.Bowman, S.E.J.

(2025) bioRxiv 

  • DOI: https://doi.org/10.1101/2025.06.12.659325
  • Primary Citation of Related Structures:  
    9P12, 9P13, 9P14, 9P15, 9P16, 9P17

  • PubMed Abstract: 

    Room-temperature (RT) X-ray diffraction experiments enable us to investigate protein dynamics, efficiently probe fragment binding, and perform time-resolved crystallography experiments. The Versatile Macromolecular Crystallography in-situ (VMXi) beamline at Diamond Light Source (DLS) in the United Kingdom specializes in the collection of RT X-ray diffraction data in situ directly from crystallization trays without any manipulation of protein crystals, improving crystal integrity for fragile crystals. While many X-ray sources are now equipped to grow crystals on site for in-situ experiments, to date there has been no comprehensive analysis that we are aware of on the effect of shipping crystals on plates at ambient temperature for RT data collection, while the equivalent methodology for cryo-cooled crystals is well established. Here we examine the impact of shipping on crystals grown on MiTeGen In Situ-1 plates at the University of Buffalo Hauptman Woodward Research Institute (UB-HWI) in Buffalo, NY, United States transatlantic to DLS in Didcot, United Kingdom. We utilized the Stanford Synchrotron Radiation Lightsource (SSRL) Blue Box Thermal Shipper (Blue Box), which can maintain temperature for up to 168 hours, to ship crystallization plates at room temperature from UB-HWI to DLS. We hypothesized that long-distance shipping might compromise data quality through mechanical stress or temperature fluctuations. Instead, we found that room-temperature data collected at VMXi showed no significant differences for crystals set up at UB-HWI and shipped relative to crystals set up on site in the UK. High-resolution structures were successfully determined for all proteins in the study, demonstrating that long-distance shipment of crystals at non-cryogenic temperatures is feasible without compromising diffraction quality. This study provides a proof-of-concept workflow for expanding access to room-temperature crystallography worldwide, enabling more researchers to leverage cutting-edge techniques without needing to grow crystals on site.


  • Organizational Affiliation
    • University at Buffalo Hauptman Woodward Institute, 700 Ellicott Street, Buffalo, NY, 14203, United States.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thaumatin I207Thaumatococcus danielliiMutation(s): 0 
UniProt
Find proteins for P02883 (Thaumatococcus daniellii)
Explore P02883 
Go to UniProtKB:  P02883
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02883
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TLA
Query on TLA

Download Ideal Coordinates CCD File 
B [auth A]L(+)-TARTARIC ACID
C4 H6 O6
FEWJPZIEWOKRBE-JCYAYHJZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free:  0.190 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.159 (Depositor), 0.157 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.2α = 90
b = 58.2β = 90
c = 150.445γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
MOLREPphasing
Cootmodel building
xia2.multiplexdata reduction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM141273

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release